Guys I think you missed his point.
To play a surface ship just click on "American Campaign" if your ship historically was of the allies side, while click on German Campaign if your ship was on the axis side.
Remember that in JSGME you should enable the ship mod last in order to make it work.
And once you are in the selection screen of the Campaign (where it asks for the name) just mess around with dates, command base and look for the ship you modded in.
Hope this was clear enough